MolNFT v1 · #79219 · protein
Crystal structure of the quinone form of methylamine dehydrogenase in complex with the diferric form of maug
3SWS · Methylamine utilization protein maug: “Crystal structure of the quinone form of methylamine dehydrogenase in complex with the diferric form of maug”. X-ray diffraction, 3 ligands (HEC, NA, CA), 20 pockets (best druggability 0.87).…
- PDB
- 3SWS
- Type
- protein
- Length
- 1,711 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methylamine utilization protein maug; Methylamine dehydrogenase light chain; Methylamine…
- EC
- 1.-.-.-, 1.4.99.3
- UniProt
- Q51658, P22619, A1BB97
- Ligands
- HEC, NA, CA
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 21% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Methylamine utilization protein maug (EC 1.-.-.-) | protein | 354 | 44% helix, 8% strand | Q51658 |
| C | Methylamine dehydrogenase light chain (EC 1.4.99.3) | protein | 126 | 10% helix, 33% strand | P22619 |
| D, F | Methylamine dehydrogenase heavy chain (EC 1.4.99.3) | protein | 376 | 7% helix, 47% strand | A1BB97 |
| E | Methylamine dehydrogenase light chain (EC 1.4.99.3) | protein | 125 | 10% helix, 30% strand | P22619 |
Ligands and binding sites
- HEC · Heme C · ligand · 4 copies · chains A, B
- NA · Sodium ion · metal · 4 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B, C, D
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains D
- ACT · Acetate ion · additive · chains D
- 1PE · Pentaethylene glycol · additive · chains D
- PG4 · Tetraethylene glycol · additive · chains F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 694 | 0.87 | 0.91 | 91 | CA, HEC |
| 2 | 681 | 0.87 | 0.91 | 87 | CA, HEC |
| 3 | 247 | 0.81 | 0.93 | 38 | empty |
| 4 | 247 | 0.81 | 0.93 | 40 | empty |
| 5 | 984 | 0.77 | 0.80 | 102 | EDO |
Interfaces
11 interfaces between chains.
- E–F · 1676 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 1670 Ų buried · 28 hydrogen bonds · protein-protein
- C–F · 1337 Ų buried · 20 hydrogen bonds · protein-protein
- D–E · 1289 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 954 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 8 cofactor, 2 modified (disulfide, heme c attachment, cofactor).
Compared structures
- 3SWS · Crystal Structure of the Qui Form of Methylamine Dehydrogenase in Complex with the… · the same entry in another collection · chain F against F, TM-score 1.00
- Q51658 · AlphaFold monomer V2.0 prediction for methylamine utilization protein maug (Q51658) · a predicted model of the same protein · chain A against A, TM-score 1.00
- P22619 · AlphaFold monomer V2.0 prediction for methylamine dehydrogenase light chain (P22619) · a predicted model of the same protein · chain E against A, TM-score 0.99
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q51658
- Every structure of UniProt P22619
- Every structure of UniProt A1BB97
- Elsewhere: RCSB PDB 3SWS · PDBe 3SWS · UniProt Q51658 · UniProt P22619 · UniProt A1BB97
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